DNA is the genetic material found in chromosomes inside cells. It contains the biological instructions that determine traits like eye color. DNA is made of nucleotides with a phosphate group, sugar (deoxyribose), and one of four nitrogenous bases: adenine, guanine, cytosine, or thymine. DNA exists as two strands coiled around each other in the famous double helix structure, with the bases on one strand pairing with their complements on the other strand. Molecular techniques use DNA, RNA, and enzymes to study biology at a molecular level and detect disease states.

1. M.PRASAD NAIDU
Msc Medical Biochemistry,
Ph.D Research scholar.

2. Explain in your own words, what is DNA?
1. DNA is deoxyribonucleicantidisestablishmentarianism, a
complex string of syllables found inside your body in tiny
genes called chromosomes.
2. The information in your DNA determines your unique
biological characteristics, such as eye color, Social Security
number, and age. There is surprisingly little difference
between DNA in humans, Democrats, and Republicans.

4. 1. WHOLE ORGANISMS
2. ORGANS
3. TISSUES
4. CELLS
5. INTRACELLULAR ORGANELLES
6. CHEMICAL COMPONENTS

5. 1. PROTEINS
2. LIPIDS
3. NUCLEIC ACIDS:
• DNA
• RNA

6. Molecular biology techniques utilize
DNA, RNA, and enzymes that
interact with nucleic acids to
understand biology at a molecular
level.

7. Molecular Pathology is a subspecialty of
pathology that utilizes molecular biology
techniques to:
Detect normal and disease states
(diagnosis)
Predict disease progression (prognosis)

8. INHERITED DISEASES (GENETICS)
› Cystic fibrosis
› Sickle cell anemia
› Predispositions to cancer
INFECTIOUS DISEASES
› Bacteria
› Viruses
› Fungi

9. HEMATOPATHOLOGY
› Leukemias
› Lymphomas
SOLID TUMORS
› Breast cancer
› Colon cancer
› Brain cancer

10. FORENSICS
IDENTITY TESTING
› HLA
› parentage

11.  Genetic material of all known organisms
 DNA: deoxyribonucleic acid
 RNA: ribonucleic acid (e.g., some viruses)
 Consist of chemically linked sequences of
nucleotides
 Nitrogenous base
 Pentose- 5-carbon sugar (ribose or
deoxyribose)
 Phosphate group
 The sequence of bases provides the genetic
information

12.  Two types of bases
 Purines are fused five- and six-membered rings
 Adenine A DNA RNA
 Guanine G DNA RNA
 Pyrimidines are six-membered rings
 Cytosine C DNA RNA
 Thymine T DNA
 Uracil U RNA

13.  Hydrogen bonds are relatively weak bonds
compared to covalent bonds
 Hydrogen bonds can form between a pyrimidine
and a purine
 Watson-Crick base-pairing rules
 A T
 G C

14. H
H
H H
O
O
H
C
C
C C
N
N
C
Thymine
H
N
H
H
N
C C
C
C
N
N H
N
C
Adenine
H
O
N
H C
C C
N
N
C
Cytosine
H
H
H
N
C C
C
C
N
N H
N
C
Guanine
N
H
O
H

15. 5’ 5’
3’
3’
In general, DNA is double-stranded.
Double-stranded (ds) DNA takes the
form of a right handed helix with
approximately 10 base pairs per turn of
the helix.

16.  In the DNA double helix, purines and pyrimidines
face each other
 The two polynucleotide chains in the double helix
are connected by hydrogen bonds between the
bases
 Watson-Crick base-pairing rules
 A T
 G C
 GC base pairs (bps)have more energy than AT
bps
 Since one strand of DNA is complementary to the
other, genetic material can be accurately
reproduced; each strand serves as the template
for the synthesis of the other

17. 5’p OH3’
3’OH p5’
Two strands of the DNA double helix are
antiparallel and complementary to each
other

18. promoter Structural gene
flank flank
upstream downstream
5’ 3’
•A gene is a unit of inheritance
•Carries the information for a:
-polypeptide
-structural RNA molecule

19. Endonuclease
5’ Exonuclease 3’ Exonuclease

20.  Specific endonucleases
 Recognize specific short sequences of DNA and
cleave the DNA at or near the recognition
sequence
 Recognition sequences: usually 4 or 6 bases but
there are some that are 5, 8, or longer
 Recognition sequences are palindromes
 Palindrome: sequence of DNA that is the same
when one strand is read from left to right or the
other strand is read from right to left– consists of
adjacent inverted repeats

21.  Example of a palindrome:
GAATTC
CTTAAG
 Restriction enzymes are isolated from bacteria
 Derive names from the bacteria
 Genus- first letter capitalized
 Species- second and third letters (small case)
 Additional letters from “strains”
 Roman numeral designates different enzymes from the
same bacterial strain, in numerical order of discovery
 Example: EcoRI
 E Escherichia
 Co coli
 R R strain
 I first enzyme discovered from Escherichia coli R

22.  Nucleic acid hybridization is the formation of a
duplex between two complementary sequences
 Intermolecular hybridization: between two
polynucleotide chains which have complementary
bases
› DNA-DNA
› DNA-RNA
› RNA-RNA
 Annealing is another term used to describe the
hybridization of two complementary molecules

23. Double-
stranded
DNA
Denaturation
Single-
stranded
DNA
Initial
Base
pairing
Renatured
DNA
Renaturation

24.  Probe is a nucleic acid that
› can be labeled with a marker which allows
identification and quantitation
› will hybridize to another nucleic acid on the basis of
base complementarity
 Types of labels
› Radioactive (32P, 35S, 14C, 3H)
› Fluorescent
 FISH: fluorescent in situ hybridization
 chromosomes
› Biotinylated (avidin-streptavidin)

25.  Solid support hybridization: DNA or RNA is
immobilized on an inert support so that self-
annealing is prevented
 Bound sequences are available for hybridization
with an added nucleic acid (probe).
 Filter hybridization is the most common
application:
 Southern Blots
 Dot/Slot Blots
 Northern Blots
 In-silica hybridization (glass slides)
 in situ hybridization (tissue)
 Chromosomal (FISH)
 Microarrays

26.  Southern blotting is a procedure for transferring
denatured DNA from an agarose gel to a solid
support filter where it can be hybridized with a
complementary nucleic acid probe
 The DNA is separated by size so that specific
fragments can be identified
 Procedure:
› Restriction digest to make different sized fragments
› Agarose gel electrophoresis to separate by size
› Since only single strands bind to the filter, the DNA
must be denatured.
› Denaturation to permit binding to the filter (NaOH)
› Transfer to filter paper (capillary flow)
› Hybridization to probe
› Visualization of probe

27. Restriction enzyme
DNA of
various sizes
Electrophorese on agarose gel
gel
Denature - transfer to
filter paper.
blot

28. Hybridize to probe
Visualize
Denature- transfer to
filter paper.
blot

29. Southern Blot

30.  DNA or RNA is bound directly to a solid support
filter
 No size separation
 Ideal for multiple samples and quantitative
measurements
 Important to establish specificity of conditions

31. Slot Blot

32. This electronic microarray is an example of "Lab-on-a-Chip"
technology. It is an electrophoresis device that produces
results up to 1000 times faster than conventional techniques
while using much less sample.

33. Control Signals
Region-Specific Signal
The chromosome banding technique performed 20 years ago missed the
small deletion. High resolution banding developed more recently can
elucidate the abnormality. Fluorescence in situ Hybridization (FISH) is a
powerful technique in that it can reveal submicroscopic abnormalities even
in non-dividing cells.

34.  PCR is the in vitro enzymatic
synthesis and amplification of
specific DNA sequences
 Can amplify one molecule of DNA
into billions of copies in a few
hours

35.  Detection of chromosomal translocations
› Amplification across a translocation sequence
 Chromosome painting
 Detection of residual disease
 Infectious disease
 Forensics
 HLA typing
 Detection of Loss of Suppressor Genes
› Loss of Heterozygosity (LOH)

36.  Genome: The entire DNA of an organism
› Humans
 diploid (chromosome pairs)
 6 x 109 bp per diploid genome
 Haploid genome is one set of chromosomes
 Chromosome: structure found within a cell
nucleus consisting of a continuous length of ds
DNA
› Humans
 22 pairs of autosomal chromosomes
 2 sex chromosomes

37. 40,000 genes
Speaking a language of molecular
fingerprints
Gene expression is another
language of complexity

38.  Locus: a position on a
chromosome
 Allele: alternate form of DNA at a
specific locus on the chromosome
 Each individual inherits two copies
of DNA
 Maternal
 Paternal
 Homozygous alleles: the two copies
are identical
 Heterozygous alleles: the two copies
are different

39.  RFLP is a polymorphic allele identified by the
presence or absence of a specific restriction
endonuclease recognition site:
› GAATTC versus GATTTC
 RFLP is usually identified by digestion of genomic
DNA with specific restriction enzymes followed
by Southern blotting
 Regions of DNA with polymorphisms:
› Introns
› Flanking sequences
› Exons

40.  Most genes have small sequence
differences between individuals
 Occur every 1350 bp on average
 Some of these polymorphisms may affect:
 How well the protein works
 How the protein interacts with another protein
or substrate
 The different gene forms containing
polymorphisms are called alleles

41.  Sequence DNA
 Hybridization Methods
› Blotting
› Chips
 Restriction enzyme polymorphisms:
› GAATTC versus GATTTC
 SNPs (single nucleotide polymorphisms)

42. Single nucleotide polymorphisms
Distinction from mutations

43. Allele Specific Oligonucleotides
ATGTGGCCATGTGGC
ATGCGGCCATGTGGC
ASOs can be used to detect SNPs
(single nucleotide polymorphisms)

44. SNPs in exons are called coding
SNPs
SNPs in introns or regulatory regions
may affect transcription,
translation, RNA stability, RNA
splicing

45. Cytochrome P450
Uptake and metabolsim of drugs
Seizure disorders
Psychiatric disorders
Cancer therapy

46. aRA
r = 0.91
log10(ratio),T3-3
Microarrays
FISH
Laser microscopegenome
Tissue arrays